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fishtree

The goal of fishtree is to provide an easy interface in R to the Fish Tree of Life API, to download taxonomies, phylogenies, diversification rate information, and other data for ray-finned fishes. It should seamlessly integrate with the rest of the R ecosystem, especially the package ape.

Example

See a list of taxa available to download.

 library(fishtree)
 
tax <- fishtree_taxonomy()
 head(tax)
 #> rank name
 #> 1 class Actinopteri
 #> 2 class Cladistia
 #> 3 subclass Chondrostei
 #> 4 subclass Neopterygii
 #> 5 infraclass Holostei
 #> 6 infraclass Teleostei

Retrieve a phylogeny for the surgeonfishes and plot the phylogeny and lineage through time plot.

 library(ape)
phy <- fishtree_phylogeny(rank = "Acanthuridae")
phy
 #> 
 #> Phylogenetic tree with 67 tips and 66 internal nodes.
 #> 
 #> Tip labels:
 #> Acanthurus_mata, Acanthurus_blochii, Acanthurus_xanthopterus, Acanthurus_bariene, Acanthurus_dussumieri, Acanthurus_leucocheilus, ...
 #> 
 #> Rooted; includes branch lengths.

 par(mfrow=c(2, 1))
 plot(phy, show.tip.label = FALSE)
 ltt.plot(phy)

You can also check out the vignettes for more detailed examples.

Installation

You can install the released version of fishtree from CRAN with:

 install.packages("fishtree")

Alternatively, download the development version with devtools:

 if (!requireNamespace("remotes", quietly = TRUE))
 install.packages("remotes")
 
remotes::install_github("jonchang/fishtree")

References

To cite fishtree in publications use:

Chang, J., Rabosky, D. L., Smith, S. A., & Alfaro, M. E. (2019). An R package and online resource for macroevolutionary studies using the ray‐finned fish tree of life. Methods in Ecology and Evolution, 10(7) 1118-1124. doi: 10.1111/2041-210x.13182

The primary data source for fishtree was published as a part of:

Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kaschner, K., Garilao, C., Near, T. J., Coll, M., Alfaro, M. E. (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395. doi: 10.1038/s41586-018-0273-1

License

The fishtree package is licensed under a 2-clause BSD license.

Sponsorship

Please consider sponsoring the maintenance of fishtree via GitHub Sponsors.

Releasing

withr::with_envvar(c("NOT_CRAN" = "true"), devtools::release())